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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3q6k

2.520 Å

X-ray

2011-01-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:43.2 kDa salivary protein
ID:Q5WPU9_LUTLO
AC:Q5WPU9
Organism:Lutzomyia longipalpis
Reign:Eukaryota
TaxID:7200
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:41.096
Number of residues:27
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1161113.750

% Hydrophobic% Polar
36.3663.64
According to VolSite

Ligand :
3q6k_2 Structure
HET Code: SRO
Formula: C10H13N2O
Molecular weight: 177.223 g/mol
DrugBank ID: DB08839
Buried Surface Area:74.79 %
Polar Surface area: 63.66 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 2

Mass center Coordinates

XYZ
37.9052-24.1092-12.3195


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CE3CBTHR- 293.940Hydrophobic
CACG2THR- 293.430Hydrophobic
CZ2CBTYR- 904.010Hydrophobic
CE3CD1ILE- 27840Hydrophobic
OHOTHR- 3272.53123.8H-Bond
(Ligand Donor)
OHOG1THR- 3273.27147.54H-Bond
(Ligand Donor)
NZOG1THR- 3272.75161.29H-Bond
(Ligand Donor)
CACBTHR- 3274.460Hydrophobic
NZOPHE- 3442.88125.7H-Bond
(Ligand Donor)
CACD2PHE- 3443.40Hydrophobic